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@simularium Simularium

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    20 repositories

    • simularium-viewer

      Public
      NPM package to view Simularium trajectories in 3D
      TypeScript
      •
      Apache License 2.0
      •2•3•55•6•Updated Jan 1, 2026Jan 1, 2026

    • simularium-website

      Public
      Front end website for the Simularium project, includes the Simularium viewer
      TypeScript
      •
      Apache License 2.0
      •5•7•56•8•Updated Jan 1, 2026Jan 1, 2026

    • subcell-pipeline

      Public
      Simulation, analysis, and visualization functionality for subcellular models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•2•3•Updated Jan 1, 2026Jan 1, 2026

    • binding-sim-edu

      Public
      TypeScript
      •
      Other
      •0•0•21•2•Updated Dec 5, 2025Dec 5, 2025

    • simulariumio

      Public
      Python package that converts simulation outputs to the format consumed by the Simularium viewer website
      Python
      •
      Apache License 2.0
      •5•5•21•4•Updated Dec 3, 2025Dec 3, 2025

    • metrics-calculator

      Public
      [pre-release] Calculate plot metrics from spatial agent data
      Python
      •
      Apache License 2.0
      •0•0•2•0•Updated Dec 3, 2025Dec 3, 2025

    • readdy-models

      Public
      Tools for building computational biology models in ReaDDy.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•11•4•Updated Mar 28, 2025Mar 28, 2025

    • nbsv

      Public
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Jan 16, 2025Jan 16, 2025

    • subcell-website

      Public
      Website for subcellular models
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Dec 19, 2024Dec 19, 2024

    • SimulariumXR

      Public
      Unity VR/AR project for Simularium data
      C#
      •
      Apache License 2.0
      •1•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • Cytosim

      Public
      A fork of Cytosim, a cytoskeleton simulation engine (from https://gitlab.com/f-nedelec/cytosim)
      C++
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Aug 30, 2024Aug 30, 2024

    • trajectory-compare

      Public
      Prototype web pages for comparing simulation trajectories.
      JavaScript
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 17, 2024Feb 17, 2024

    • simularium-data-library

      Public
      View lists of .simularium files in public AWS S3 buckets and load them in the Simularium viewer.
      HTML
      •
      Apache License 2.0
      •307•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • simularium-planning

      Public
      Apache License 2.0
      •0•0•94•0•Updated Feb 5, 2024Feb 5, 2024

    • simularium-autoconversion

      Public
      Apache License 2.0
      •0•0•5•0•Updated Jul 11, 2023Jul 11, 2023

    • simularium-lambdas

      Public
      AWS Lambda functions for Simularium
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 11, 2023Jul 11, 2023

    • vivarium-models

      Public
      Python
      •
      Apache License 2.0
      •1•0•7•4•Updated May 23, 2023May 23, 2023

    • simularium-engine

      Public
      C++ back end application that interfaces with biological simulation engines and serves simulation data to the front end website
      C++
      •
      Apache License 2.0
      •0•0•16•0•Updated Apr 21, 2023Apr 21, 2023

    • medyan

      Public
      C++
      •
      Other
      •1•0•0•0•Updated Jun 8, 2022Jun 8, 2022

    • PhysiCell

      Public
      PhysiCell: Scientist end users should use latest release! Bugfixes should be submitted to the development branch.
      C++
      •113•0•0•0•Updated Apr 20, 2020Apr 20, 2020